3HE0 | pdb_00003he0

The Structure of a Putative Transcriptional Regulator TetR Family Protein from Vibrio parahaemolyticus.

• PDB DOI: https://doi.org/10.2210/pdb3HE0/pdb

• Classification: transcription regulator
• Organism(s): Vibrio parahaemolyticus
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2009-05-07 Released: 2009-07-07 
• Deposition Author(s): Cuff, M.E., Hendricks, R., Moy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.227 (Depositor), 0.245 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Literature

The Structure of a Putative Transcriptional Regulator TetR Family Protein from Vibrio parahaemolyticus.

Cuff, M.E., Hendricks, R., Moy, S., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 67.84 kDa 
• Atom Count: 4,645 
• Modeled Residue Count: 546 
• Deposited Residue Count: 588 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator, TetR family	A, B, C	196	Vibrio parahaemolyticus	Mutation(s): 0  Gene Names: VP0040
UniProt
Find proteins for Q87TM9 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)) Explore Q87TM9  Go to UniProtKB:  Q87TM9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth A], F [auth A], J [auth B], K [auth B], L [auth B], Q [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	G [auth A], H [auth A], M [auth B], N [auth B], O [auth B], R [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	I [auth A], P [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.227 (Depositor), 0.245 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.272	α = 90
b = 95.548	β = 90
c = 190.541	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building
CCP4	phasing
O	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-07 
Deposition Author(s): Cuff, M.E., Hendricks, R., Moy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-07-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary